Mooney was a coal miner’s son who became an apprentice iron moulder at the age of 14 and a member of the iron moulders’ union not long after. He became committed to Socialist politics after several trips to Europe, joined the Industrial Workers of the World (IWW), and helped to publish Revolt, a Socialist newspaper. During 1913–14 in California he and Warren Knox Billings, a young drifter from New York, were involved in a long, violent strike of electrical workers against the Pacific Gas and Electrical Company. Billings was arrested for carrying dynamite and briefly imprisoned; Mooney was arrested on similar charges but acquitted.

In 1916 Mooney, his wife Rena Ellen Mooney (née Hermann), Billings, and several others were all indicted and convicted for the bombing of the Preparedness Day Parade in San Francisco, which killed 10 people and injured 40 others. The death sentence passed on Mooney set off protests and agitations that lasted two decades and that led, first, to the commutation of the sentence to life imprisonment and, then, to a pardon by the governor of California in 1939. (He was officially pardoned in 1961). A report on the Mooney-Billings case prepared in 1931 by the National Commission on Law Observance and Enforcement cast serious doubt on the evidence that led to Mooney’s conviction.